Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate GFF427 Psest_0431 Lactate dehydrogenase and related dehydrogenases
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__psRCH2:GFF427 Length = 336 Score = 200 bits (508), Expect = 5e-56 Identities = 112/332 (33%), Positives = 182/332 (54%), Gaps = 14/332 (4%) Query: 1 MKPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE 60 M PK+ IT ++ + ++++ E+ + PR +L + R+ A++ + D+VD + Sbjct: 1 MLPKLVITHRVHDEILQLLAPHCELMTNQTDSTLPREEILRRCRDAQAMMAFMPDRVDAD 60 Query: 61 LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 L+ P+L+++ G+DN D++ T RG+++T P +LT TA+LA L + + R + Sbjct: 61 FLQACPELRVVGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLR 120 Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYY- 179 ADAFVRSG+++ GW P F G GL T+GI+G G IG A+A R +G+G + Y+ Sbjct: 121 AADAFVRSGKFQ----GWQP-QFYGTGLDNATVGILGMGAIGLAMADRLQGWGATLQYHE 175 Query: 180 SRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239 ++ + E+ +G V L SDFI L +PL +T H++ + L L++P A+L+N Sbjct: 176 AKALDTQTEQRLGLRRVACSELFASSDFILLALPLNADTQHLVNAELLALVRPGALLVNP 235 Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEE--------LFKLKNVVLAPHIGS 291 RG+VVD A++ AL+ G + G DVFE E + + L N + PHIGS Sbjct: 236 CRGSVVDEAAVLAALERGQLGGYAADVFEMEDWARADRPRLIDPALLAHPNTLFTPHIGS 295 Query: 292 ATHEAREGMAELVAKNLIAFAKGEIPPNLVNK 323 A R + A+N+I G P N N+ Sbjct: 296 AVRAVRLEIERCAAQNIIQALAGARPINAANR 327 Lambda K H 0.317 0.137 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 224 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 331 Length of database: 336 Length adjustment: 28 Effective length of query: 303 Effective length of database: 308 Effective search space: 93324 Effective search space used: 93324 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory